Investigating RND efflux pumps in <i>Sphingobium yanoikuyae</i> P4: the role of nonpathogenic bacteria in antibiotic resistance gene spread amid environmental contamination

The widespread and inappropriate application of antibiotics across human and veterinary medicine has generated pressing global health threats, principally the emergence of antimicrobial resistance (AMR) and the contamination of the environment with antibiotics. A fundamental mechanism fueling environmental AMR is the proliferation and horizontal dissemination of antibiotic resistance genes (ARGs), with efflux transporter proteins functioning as central intermediaries. Surprisingly, nonpathogenic bacteria, which are usually regarded as harmless, now pose a substantial risk to society due to the presence of efflux transporters, which make them AMR contributors. In this study, the genomic analysis of the nonpathogenic soil bacterium <i>Sphingobium yanoikuyae</i> P4 revealed an RND (Resistance-Nodulation-Division) efflux pump containing the relevant domains responsible for antibiotic efflux. Molecular docking studies revealed high affinities between the efflux pump and various antibiotics, including fluoroquinolones, beta-lactams, and sulfonamides, raising the possibility of their efflux into the environment. Antibiotic susceptibility tests showed reduced susceptibility due to the action of this efflux transporter. Furthermore, the genome analysis suggested the presence of mobile genetic elements and plasmid-associated sequences, indicating possible horizontal gene transfer. The data highlights that both nonpathogenic and pathogenic bacteria are crucial for capturing and transmitting antibiotic-resistance genes. These results confirm the disregard for existing concerns over the substantial role of nonpathogenic environmental bacteria in the ecological resistome and warrant the need to consider such microorganisms in monitoring and controlling AMR.